Occasionally, after i do a forced reboot on my iphone (holding power and home) all the apps rearrange themselves to alphabetical order and it removes all my folders. Is there a way to fix this? I have a jailbroken iPhone 3gs 4.1.2
Since your phone is jailbroken, there's no telling what's installed on the phone, so getting help for the issue may be problematic.
That said, there is an option in Settings to reset your Home Screen, which is what you're seeing. My bet is there's a flag somewhere that does that when the phone is reset.